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Downloads and Upgrades: Strand NGS, Reactome Pathway Browser, and More


Strand Life Sciences has released version 2.0 of its next-generation sequencing data analysis and visualization platform, Avadis NGS, which it has renamed Strand NGS.

The release combines features from Avadis NGS and the GeneSpring NGS. It includes a methyl-seq workflow, direct access to BioCyc and WikiPathways, better support for target enrichment experiments, and multi-omic pathway analysis.

The developers of the Reactome database have a new Reactome Pathway Browser that provides an integrated suite of tools for pathway analysis.

Features in the tool let users map protein lists to Reactome pathways, perform pathway over representation analysis for gene sets, colorize pathway diagrams with gene expression data, and compare model organism and human pathways.

BioJava Legacy 1.9.0 is now available from the project page and from the maven central repository.

A new version of RINalyzer for Cytoscape 3.1 is available. RINalyzer is a tool for analyzing and visualizing residue interaction networks (RIN) that are generatedfrom 3D protein structures. This new version of the tool includes automatic import, generation, and annotation of RINs as well as new and user-friendly means to explore and compare RINs.

Also, the Resource for Biocomputing, Visualization, and Informatics group at the University of California, San Francisco have released cddApp, a Cytoscape3 extension that supports the annotation of protein networks with information about domains and specific functional sites from the National Center for Biotechnology Information's Conserved Domain Database

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.